#!/usr/bin/env cwl-runner
### Medicare raw data federation tool
# Copyright (c) 2021. Harvard University
#
# Developed by Research Software Engineering,
# Faculty of Arts and Sciences, Research Computing (FAS RC)
# Author: Michael A Bouzinier
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
cwlVersion: v1.2
class: CommandLineTool
baseCommand: [python, -m, cms.tools.mcr_combine_tables]
doc: |
This tool combines disparate tables with raw Medicare data into a single
view, transforming common columns to uniform type and format
inputs:
database:
type: File
doc: Path to database connection file, usually database.ini
inputBinding:
prefix: --db
connection_name:
type: string
doc: The name of the section in the database.ini file
inputBinding:
prefix: --connection
table:
type: string
doc: the name of the table to be created
inputBinding:
prefix: --table
depends_on:
type: File?
doc: a special field used to enforce dependencies and execution order
outputs:
log:
type: File
outputBinding:
glob: "*.log"
errors:
type: stderr
stderr: mcr_combine_tables.err